Contacts of the helix formed by residues 646 - 658 (chain A) in PDB entry 3NC0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 646 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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644A GLN* 3.2 15.6 + - - +
645A THR* 1.3 77.7 + - - +
647A GLN* 1.3 69.5 + - - +
648A THR* 3.5 15.2 + - - -
649A VAL* 3.1 31.9 + - - +
650A GLN* 3.0 23.1 + - - +
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Residues in contact with GLN 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A THR 3.1 8.8 + - - +
646A ASP* 1.3 73.6 + - - +
648A THR* 1.3 68.8 + - + +
650A GLN* 3.2 9.1 + - - +
651A GLU* 2.8 51.0 + - - +
705A PRO* 6.2 0.3 - - - +
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Residues in contact with THR 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646A ASP* 3.5 12.1 + - - -
647A GLN* 1.3 84.1 - - - +
649A VAL* 1.3 65.4 + - - +
651A GLU* 3.2 15.8 + - - +
652A HIS* 3.3 11.4 + - - +
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Residues in contact with VAL 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A GLN* 4.0 19.5 - - + +
646A ASP* 3.1 24.4 + - - +
647A GLN 3.4 0.4 - - - -
648A THR* 1.3 79.2 - - - +
650A GLN* 1.3 67.4 + - - +
652A HIS* 3.1 8.6 + - + +
653A LEU* 3.0 41.0 + - + +
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Residues in contact with GLN 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A ILE* 2.8 37.2 + - + +
642A GLY* 3.6 16.2 + - - -
644A GLN* 3.0 27.7 + - + +
645A THR* 4.8 5.6 - - - +
646A ASP 3.0 12.9 + - - +
647A GLN* 3.7 9.2 - - - +
649A VAL* 1.3 76.8 - - - +
651A GLU* 1.3 56.9 + - + +
653A LEU* 3.5 10.2 + - - +
654A ILE* 3.0 40.3 + - + +
702A VAL* 4.6 2.2 - - - +
705A PRO* 3.4 35.9 - - - +
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Residues in contact with GLU 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647A GLN* 2.8 50.7 + - - +
648A THR* 3.4 11.3 - - - +
649A VAL 3.1 0.2 - - - -
650A GLN* 1.3 76.0 - - + +
652A HIS* 1.3 65.1 + - - +
654A ILE* 3.3 9.8 + - + +
655A GLU* 3.0 24.8 + - - +
708A ILE* 3.8 35.8 - - + +
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Residues in contact with HIS 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A THR 3.3 8.2 + - - +
649A VAL* 3.1 10.6 + - + +
651A GLU* 1.3 74.7 - - - +
653A LEU* 1.3 66.7 + - + +
655A GLU* 3.3 17.5 + - + +
656A LYS* 3.2 26.5 + - + +
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Residues in contact with LEU 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A VAL* 5.0 2.7 - - + -
611A ILE* 3.8 25.6 - - + -
612A ASP* 4.1 10.1 - - - +
615A LEU* 3.8 28.4 - - + +
641A ILE* 3.8 21.7 - - + +
644A GLN* 3.6 36.6 - - + -
649A VAL* 3.0 27.6 + - + +
650A GLN* 3.6 6.1 - - - +
652A HIS* 1.3 78.6 - - + +
654A ILE* 1.3 57.2 + - - +
656A LYS* 3.5 1.5 + - - -
657A TYR* 2.9 30.2 + - - +
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Residues in contact with ILE 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A ILE* 3.6 17.3 - - + -
650A GLN* 3.0 38.2 + - + +
651A GLU* 3.6 8.1 - - + +
652A HIS 3.2 0.2 - - - -
653A LEU* 1.3 72.9 - - - +
655A GLU* 1.3 67.1 + - - +
657A TYR* 3.4 11.9 - - + +
658A MET* 3.1 28.5 + - + +
702A VAL* 4.1 15.0 - - + -
705A PRO* 3.6 30.7 - - + +
706A PHE* 4.4 5.8 - - + +
708A ILE* 3.6 24.0 - - + -
709A GLN* 4.6 15.0 - - + +
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Residues in contact with GLU 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651A GLU 3.0 16.4 + - - +
652A HIS* 3.3 17.8 + - + +
654A ILE* 1.3 80.7 - - - +
656A LYS* 1.3 56.4 - - - +
658A MET* 3.6 3.7 + - - +
659A LEU* 3.3 30.3 + - + +
708A ILE* 5.5 7.9 - - + +
709A GLN* 6.0 0.9 - - - -
712A ARG* 4.6 20.1 + - - +
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Residues in contact with LYS 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A LEU* 3.6 42.6 + - + +
616A ASN* 2.9 31.1 + - - +
618A ILE* 5.2 3.6 - - - +
652A HIS* 3.2 18.0 + - + +
653A LEU* 4.1 3.1 - - - +
655A GLU* 1.3 75.6 - - - +
657A TYR* 1.3 66.6 + - - +
658A MET 3.2 1.3 - - - -
659A LEU* 3.2 35.5 + - + +
660A LEU* 4.5 8.3 + - - +
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Residues in contact with TYR 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A LEU* 4.2 12.9 - - + +
618A ILE* 4.5 4.8 - - + +
634A TYR* 2.5 77.0 + + - -
637A VAL* 3.8 28.5 - - + -
638A GLY* 3.2 11.9 - - - -
641A ILE* 4.2 14.8 - - + -
653A LEU 2.9 20.2 + - - +
654A ILE* 3.4 12.6 - - + +
656A LYS* 1.3 77.6 - - - +
658A MET* 1.3 71.1 + - + +
659A LEU 3.6 0.5 + - - -
660A LEU 4.8 0.3 + - - -
661A PRO* 4.2 0.2 - - - +
698A ALA* 3.0 39.8 - - + +
702A VAL* 3.7 19.5 - - + -
706A PHE* 5.2 0.7 - + - -
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Residues in contact with MET 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634A TYR* 4.8 6.5 - - - -
654A ILE* 3.1 18.1 + - + +
655A GLU* 3.7 4.9 - - - +
656A LYS 3.2 0.2 - - - -
657A TYR* 1.3 98.3 - - + +
659A LEU* 1.3 62.6 + - - +
660A LEU 3.5 1.8 - - - -
661A PRO* 3.6 21.3 - - + +
662A ASN* 3.1 26.1 + - - +
694A THR* 4.9 2.2 - - + -
695A ASN* 3.1 44.6 - - - +
698A ALA* 4.0 15.5 - - + -
706A PHE* 4.3 5.2 - - + -
709A GLN* 3.7 33.9 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il